[English] 日本語
![](img/lk-miru.gif)
- PDB-5lk6: Crystal structure of a lipase carboxylesterase from Sulfolobus is... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5lk6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a lipase carboxylesterase from Sulfolobus islandicus | ||||||
![]() | Alpha/beta hydrolase fold-3 domain protein | ||||||
![]() | HYDROLASE / Esterase / lipase / Sulfolobus / thermostable | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schwarz-Linnet, T. / Teilum, K. / Olsen, J.G. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: EstA from Sufolobus islandicus is stabilized by mono-methylation of lysine residues Authors: Schwarz-Linnet, T. / Stiefler-Jensen, D. / de Lichetenberg, C. / Olsen, J.G. / Nguyen, T.T.T.N. / Rand, K.D. / Teilum, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 247.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 201.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3aikS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 34540.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Hyperthermophil acidophil archea Source: (gene. exp.) ![]() ![]() Strain: REY15A / Cell: Prokaryot / Cell line: E233S / Gene: SiRe_0290 / Plasmid: pSeSD Details (production host): D-Arabinose inducible promoter, shuttle vector Cell (production host): Prokaryot / Cell line (production host): E233S / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.34 % / Description: Larger than 0.2 mm |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Hampton Reaserch Crystal Screen 2 (HR2-112) Condition #23. 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane. Reservoir volume 600 uL. 2 uL of EstA 10 mg/mL in 50 mM ...Details: Hampton Reaserch Crystal Screen 2 (HR2-112) Condition #23. 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane. Reservoir volume 600 uL. 2 uL of EstA 10 mg/mL in 50 mM Tris pH 8, mixed with 2 uL of reservoir volume for hanging drop at room temperature. PH range: 6.5 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2012 Details: First mirror: Water-cooled vertically collimating cylindrical mirror (R = 7300 m). Second mirror: Toroid mirror for horizontal and vertical focusing (R = 3300 m, R = 27 mm). |
Radiation | Monochromator: Water-cooled double-crystal monochromator, Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.42 Å / Num. obs: 79041 / % possible obs: 93.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 10.62 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.4 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3AIK Resolution: 2.6→29.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.985 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.085 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.42 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|